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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ), 'gf_id' => 'HOM05D001618', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001618' ), 'data_identifier' => 'HOM05D001618', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001618', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '399', 'num_species' => '91' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40550' => 'bna', 'A02p06500' => 'bna', 'A02p17990' => 'bna', 'A03p10270' => 'bna', 'A06p13300' => 'bna', 'A07p30230' => 'bna', 'A07p38610' => 'bna', 'A08p30970' => 'bna', 'A10p19250' => 'bna', 'Aa31LG4G2760' => 'aar', 'Aa31LG8G180' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5076' => 'aag', 'Actinidia30253' => 'ach', 'Ah.09g229040' => 'amhyb', 'Ah.09g229050' => 'amhyb', 'Ah.14g084670' => 'amhyb', 'Ah.15g095080' => 'amhyb', 'Ah.16g106590' => 'amhyb', 'AL1G29600' => 'aly', 'AL2G32100' => 'aly', 'AL6G32330' => 'aly', 'Aqoxy7G01508' => 'aox', 'Aqoxy7G04145' => 'aox', 'arahy.Tifrunner.gnm1.ann1.YT59NJ' => 'arhy', 'AT1G17345' => 'ath', 'AT1G72430' => 'ath', 'AT3G12955' => 'ath', 'AT5G20820' => 'ath', 'ATR0681G270' => 'atr', 'ATR0763G232' => 'atr', 'Atru.chr1.4130' => 'acertr', 'Atru.chr12.2174' => 'acertr', 'Atru.chr7.1761' => 'acertr', 'AUR62001434' => 'cqu', 'AUR62009932' => 'cqu', 'AUR62025305' => 'cqu', 'AUR62025306' => 'cqu', 'AUR62025307' => 'cqu', 'AUR62028310' => 'cqu', 'AUR62028312' => 'cqu', 'AUR62037622' => 'cqu', 'AUR62040862' => 'cqu', 'BcaB01g04768' => 'bca', 'BcaB03g13006' => 'bca', 'BcaB03g14994' => 'bca', 'BcaB03g15665' => 'bca', 'BcaB04g21023' => 'bca', 'BcaB05g22812' => 'bca', 'BcaB05g24754' => 'bca', 'BcaB07g34031' => 'bca', 'BcaB08g36530' => 'bca', 'BcaB08g36531' => 'bca', 'BcaC03g13802' => 'bca', 'BcaC03g15375' => 'bca', 'BcaC04g19469' => 'bca', 'BcaC04g19470' => 'bca', 'BcaC05g25647' => 'bca', 'BcaC07g38847' => 'bca', 'BcaC08g45710' => 'bca', 'BcaC08g46694' => 'bca', 'BcaC09g48283' => 'bca', 'BolC1t05159H' => 'bol', 'BolC2t07074H' => 'bol', 'BolC2t09039H' => 'bol', 'BolC3t13650H' => 'bol', 'BolC5t30280H' => 'bol', 'BolC6t38597H' => 'bol', 'BolC6t39722H' => 'bol', 'BolC8t49415H' => 'bol', 'BolC9t58400H' => 'bol', 'BraA01t04090Z' => 'bra', 'BraA02t05595Z' => 'bra', 'BraA02t06846Z' => 'bra', 'BraA03t10338Z' => 'bra', 'BraA06t24483Z' => 'bra', 'BraA07t30660Z' => 'bra', 'BraA07t31419Z' => 'bra', 'BraA08t35026Z' => 'bra', 'BraA10t44002Z' => 'bra', 'C01p52190' => 'bna', 'C02p29890' => 'bna', 'C03p11790' => 'bna', 'C05p15740' => 'bna', 'C06p34980' => 'bna', 'C06p46780' => 'bna', 'C08p17840' => 'bna', 'C09p55380' => 'bna', 'CAN.G2615.1' => 'can', 'CAN.G275.4' => 'can', 'CAN.G943.36' => 'can', 'CANSAT56G1990' => 'cansat', 'CANSAT56G3735' => 'cansat', 'CANSAT80G2159' => 'cansat', 'CARHR017940' => 'chi', 'CARHR065360' => 'chi', 'CARHR087480' => 'chi', 'CARHR192040' => 'chi', 'Carub.0001s1710' => 'cru', 'Carub.0002s1928' => 'cru', 'Carub.0003s1229' => 'cru', 'Carub.0006s1911' => 'cru', 'Ca_02276_v3' => 'car', 'Ca_21336_v3' => 'car', 'Ca_23415_v3' => 'car', 'Ca_30967_v3' => 'car', 'CBR_g52549' => 'cbr', 'Cc06_g12650' => 'ccan', 'Cfa002941' => 'cfa', 'Cfa003492' => 'cfa', 'Cfa019433' => 'cfa', 'Cfa019928' => 'cfa', 'Ciclev10009909m.g' => 'ccl', 'Ciclev10023709m.g' => 'ccl', 'Ciclev10026743m.g' => 'ccl', 'CiPaw.01G214100' => 'cil', 'CiPaw.02G132800' => 'cil', 'CiPaw.03G179500' => 'cil', 'CiPaw.03G201600' => 'cil', 'CiPaw.04G140000' => 'cil', 'ClCG07G014380' => 'cla', 'ClCG09G001240' => 'cla', 'ClCG11G016410' => 'cla', 'COL.COLO4_21212' => 'col', 'COL.COLO4_30830' => 'col', 'Cpa.g.c37833' => 'cpa', 'Cpa.g.sc25.171' => 'cpa', 'CsaV3_3G030900' => 'csa', 'CsaV3_4G031860' => 'csa', 'CsaV3_7G034130' => 'csa', 'CSS0001227' => 'camsi', 'CSS0017690' => 'camsi', 'CSS0034956' => 'camsi', 'DCAR_003147' => 'dca', 'DCAR_011920' => 'dca', 'DCAR_011922' => 'dca', 'DCAR_013740' => 'dca', 'Dinv19620' => 'din', 'Duzib150G0108' => 'dzi', 'Duzib160G0080' => 'dzi', 'Duzib168G1557' => 'dzi', 'Duzib187G1533' => 'dzi', 'Duzib192G0817' => 'dzi', 'Duzib213G0738' => 'dzi', 'Duzib235G0314' => 'dzi', 'Duzib268G0166' => 'dzi', 'ECA236G5106' => 'eca', 'EL10Ac2g03346' => 'bvu', 'EL10Ac7g16458' => 'bvu', 'EL10Ac8g18980' => 'bvu', 'EL10Ac8g18981' => 'bvu', 'Eucgr.C00771' => 'egr', 'Eucgr.C03200' => 'egr', 'Eucgr.C03202' => 'egr', 'Eucgr.F01454' => 'egr', 'Eucgr.I02135' => 'egr', 'FAN02G1579' => 'fan', 'FAN05G1955' => 'fan', 'FAN09G4802' => 'fan', 'FAN11G0765' => 'fan', 'FAN14G0645' => 'fan', 'FAN16G3043' => 'fan', 'FAN19G1553' => 'fan', 'FAN23G2159' => 'fan', 'FAN25G3714' => 'fan', 'FAN28G2041' => 'fan', 'FvH4_1g09300' => 'fve', 'FvH4_3g15820' => 'fve', 'FvH4_6g35410' => 'fve', 'Glyma.03G014800' => 'gma', 'Glyma.07G043500' => 'gma', 'Glyma.07G074900' => 'gma', 'Glyma.08G236300' => 'gma', 'Glyma.09G073400' => 'gma', 'Glyma.13G113800' => 'gma', 'Glyma.16G011900' => 'gma', 'Glyma.17G046000' => 'gma', 'Gohir.1Z049325' => 'ghi', 'Gohir.A01G038900' => 'ghi', 'Gohir.A05G035800' => 'ghi', 'Gohir.A05G137900' => 'ghi', 'Gohir.A06G079500' => 'ghi', 'Gohir.A07G017000' => 'ghi', 'Gohir.A10G051600' => 'ghi', 'Gohir.A13G189300' => 'ghi', 'Gohir.D01G026600' => 'ghi', 'Gohir.D05G037300' => 'ghi', 'Gohir.D05G140000' => 'ghi', 'Gohir.D06G079100' => 'ghi', 'Gohir.D07G016800' => 'ghi', 'Gohir.D10G053300' => 'ghi', 'Gohir.D13G196300' => 'ghi', 'Gorai.001G017600' => 'gra', 'Gorai.002G036000' => 'gra', 'Gorai.009G037800' => 'gra', 'Gorai.009G144300' => 'gra', 'Gorai.010G092200' => 'gra', 'Gorai.011G056900' => 'gra', 'Gorai.011G204300' => 'gra', 'Gorai.013G222500' => 'gra', 'GSVIVG01015021001' => 'vvi', 'GSVIVG01016698001' => 'vvi', 'HanXRQChr03g0078101' => 'han', 'HanXRQChr04g0125361' => 'han', 'HanXRQChr05g0160861' => 'han', 'HanXRQChr06g0178261' => 'han', 'HanXRQChr11g0335331' => 'han', 'HanXRQChr12g0354271' => 'han', 'Haze_08482' => 'cav', 'Haze_08552' => 'cav', 'Haze_16100' => 'cav', 'Haze_26064' => 'cav', 'Hma1.2p1_0090F.1_g046000' => 'hma', 'Hma1.2p1_0637F.1_g193550' => 'hma', 'HPP92_002375' => 'vpl', 'HPP92_002390' => 'vpl', 'HPP92_004360' => 'vpl', 'HPP92_010939' => 'vpl', 'HPP92_016225' => 'vpl', 'HPP92_016240' => 'vpl', 'HPP92_027602' => 'vpl', 'Lalb_Chr01g0007171' => 'lal', 'Lalb_Chr04g0253791' => 'lal', 'Lalb_Chr10g0101251' => 'lal', 'Lalb_Chr11g0074001' => 'lal', 'Lalb_Chr12g0200331' => 'lal', 'Lalb_Chr13g0299221' => 'lal', 'Lalb_Chr17g0343371' => 'lal', 'Lalb_Chr23g0276241' => 'lal', 'Lj3g0002752' => 'lja', 'Lj3g0012457' => 'lja', 'Lj4g0006286' => 'lja', 'Lj6g0007042' => 'lja', 'Lsat_1_v5_gn_1_55561' => 'lsa', 'Lsat_1_v5_gn_5_139080' => 'lsa', 'Lsat_1_v5_gn_7_112181' => 'lsa', 'Lsat_1_v5_gn_7_70901' => 'lsa', 'Lsat_1_v5_gn_8_85101' => 'lsa', 'Manes.03G043100' => 'mes', 'Manes.04G149200' => 'mes', 'Manes.11G014900' => 'mes', 'Manes.14G016100' => 'mes', 'Manes.16G092600' => 'mes', 'Mapoly0047s0021' => 'mpo', 'MBI02_g40901_MAGBIO' => 'mbi', 'MBI13_g01668_MAGBIO' => 'mbi', 'MBI19_g37997_MAGBIO' => 'mbi', 'MD02G1100200' => 'mdo', 'MD05G1219800' => 'mdo', 'MD07G1220700' => 'mdo', 'MD10G1202100' => 'mdo', 'MD15G1223100' => 'mdo', 'Medtr2g044020' => 'mtr', 'Medtr4g124700' => 'mtr', 'Medtr8g022380' => 'mtr', 'Medtr8g022440' => 'mtr', 'MELO3C010571.2' => 'cme', 'MELO3C022688.2' => 'cme', 'MELO3C024323.2' => 'cme', 'Migut.J00890' => 'egut', 'Migut.L01594' => 'egut', 'Migut.M01559' => 'egut', 'MSTRG.10488' => 'ama', 'MSTRG.14539' => 'ama', 'MSTRG.16111' => 'ama', 'MSTRG.19430' => 'ama', 'Nitab4.5_0000073g0410' => 'nta', 'Nitab4.5_0000170g0020' => 'nta', 'Nitab4.5_0001407g0020' => 'nta', 'Nitab4.5_0001407g0050' => 'nta', 'Nitab4.5_0002443g0010' => 'nta', 'Nn6g35638' => 'nnu', 'Nn7g37979' => 'nnu', 'Nn8g38539' => 'nnu', 'Oeu000295.1' => 'oeu', 'Oeu003829.1' => 'oeu', 'Oeu010849.1' => 'oeu', 'Oeu015768.1' => 'oeu', 'Oeu055328.1' => 'oeu', 'Oeu055908.1' => 'oeu', 'Os08g0452500' => 'osa', 'Os09g0437100' => 'osa', 'Os12g0609600' => 'osa', 'Peaxi162Scf00191g00051' => 'pax', 'Peaxi162Scf00452g00826' => 'pax', 'Peaxi162Scf00533g00001' => 'pax', 'Peaxi162Scf00533g00021' => 'pax', 'Peaxi162Scf00533g00022' => 'pax', 'Peaxi162Scf00928g00224' => 'pax', 'PGR083G0576' => 'pgr', 'PGR119G1512' => 'pgr', 'PGR142G3236' => 'pgr', 'PGSC0003DMG400002896' => 'stu', 'PGSC0003DMG400013549' => 'stu', 'Phvul.003G127650' => 'pvu', 'Phvul.009G223900' => 'pvu', 'Phvul.010G094500' => 'pvu', 'Phvul.010G125400' => 'pvu', 'Phvul.011G174700' => 'pvu', 'Potri.001G164300' => 'ptr', 'Potri.001G458000' => 'ptr', 'Potri.003G071000' => 'ptr', 'Potri.006G137000' => 'ptr', 'Potri.011G143400' => 'ptr', 'Prupe.3G035000' => 'ppe', 'Prupe.4G140200' => 'ppe', 'Prupe.7G192600' => 'ppe', 'Psat1g136800' => 'psa', 'Psat4g019200' => 'psa', 'Psat4g219520' => 'psa', 'Psat4g219600' => 'psa', 'PSO104G0034' => 'pso', 'PSO135G0354' => 'pso', 'PSO421G0623' => 'pso', 'PSO724G0827' => 'pso', 'PSO724G1282' => 'pso', 'QL04p073875' => 'qlo', 'QL05p001985' => 'qlo', 'QL11p002832' => 'qlo', 'RcHm_v2.0_Chr2g0095881' => 'rch', 'RcHm_v2.0_Chr2g0146941' => 'rch', 'RcHm_v2.0_Chr5g0026611' => 'rch', 'Rhsim05G0002600' => 'rsi', 'Rhsim12G0212400' => 'rsi', 'Sabra01G0128500' => 'sbr', 'Sabra03G0041900' => 'sbr', 'Sabra06G0107100' => 'sbr', 'Sabra11G0128100' => 'sbr', 'Sabra16G0310500' => 'sbr', 'SalBow5G0564' => 'sbo', 'SalBow5G1988' => 'sbo', 'SalBow6G1257' => 'sbo', 'SalBow8G1925' => 'sbo', 'Sc06g0001550' => 'sci', 'Sc08g0009120' => 'sci', 'Sc18g0002820' => 'sci', 'Sc18g0002830' => 'sci', 'Sed0002943' => 'sed', 'Sed0006972' => 'sed', 'Sed0016937' => 'sed', 'Sed0022517' => 'sed', 'Sed0024570' => 'sed', 'Sed0028153' => 'sed', 'SEGI_23969' => 'sgi', 'SGA_v2.0_scaffold186G40221' => 'sas', 'SGA_v2.0_scaffold21G09551' => 'sas', 'SGA_v2.0_scaffold281G46916' => 'sas', 'SGA_v2.0_scaffold296G47574' => 'sas', 'SMO118G0531' => 'smo', 'SMO172G0053' => 'smo', 'SMO358G0203' => 'smo', 'Solyc05g025985.1' => 'sly', 'Solyc07g042490.1' => 'sly', 'Solyc12g009290.1' => 'sly', 'Sopen05g022270' => 'spe', 'Sopen07g022120' => 'spe', 'Sopen07g034610' => 'spe', 'Sopen12g004270' => 'spe', 'Sp1g15480' => 'spa', 'Sp3g11100' => 'spa', 'Sp5g27510' => 'spa', 'Sp6g23710' => 'spa', 'SpUn0033_0070' => 'spa', 'TAR383G0482' => 'tar', 'TAR626G0752' => 'tar', 'TAR626G1833' => 'tar', 'THA.LOC104799607' => 'tha', 'THA.LOC104808064' => 'tha', 'THA.LOC104810258' => 'tha', 'THA.LOC104810984' => 'tha', 'THA.LOC104812268' => 'tha', 'Thecc.06G127100' => 'tca', 'Thecc.07G153100' => 'tca', 'Thecc.09G070700' => 'tca', 'Thhalv10009429m.g' => 'esa', 'Thhalv10015282m.g' => 'esa', 'Thhalv10019329m.g' => 'esa', 'Thhalv10022049m.g' => 'esa', 'TPR.G12663' => 'tpr', 'TPR.G16668' => 'tpr', 'TPR.G31744' => 'tpr', 'TPR.G9409' => 'tpr', 'TWI14G0119' => 'twi', 'TWI23G0248' => 'twi', 'TWI34G0338' => 'twi', 'TWI38G2010' => 'twi', 'TWI59G1334' => 'twi', 'vmacro17082' => 'vma', 'VMungo0331G0986' => 'vmu', 'VMungo0331G1754' => 'vmu', 'VMungo1127G1601' => 'vmu', 'VMungo1215G2900' => 'vmu', 'VMungo1309G1696' => 'vmu', 'Zm00001eb040610' => 'zma', 'Zm00001eb040650' => 'zma', 'Zm00001eb040680' => 'zma', 'Zm00001eb100000' => 'zma', 'Zm00001eb135850' => 'zma', 'Zm00001eb177200' => 'zma', 'Zm00001eb313920' => 'zma' ) $gf_id = 'HOM05D001618' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001618' ) $data_identifier = 'HOM05D001618' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 1, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 1, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 9, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 4, 'din' => (int) 1, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 7, 'lal' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb313920' $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